Optimal reconstruction of the folding landscape using differential energy surface analysis

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 87, Issue 3, 2013, Pages

  La Porta, Arthur ^a   Denesyuk, Natalia A ^a   De Messieres, Michel ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE MEASUREMENT; DIFFERENTIAL ENERGY; END-TO-END DISTANCES; EXPERIMENTAL SYSTEM; MAXIMUM LIKELIHOOD ESTIMATE; REACTION COORDINATES; SINGLE VALUED FUNCTIONS; WEIGHTED HISTOGRAM ANALYSIS METHOD;

EXPERIMENTS; MAXIMUM LIKELIHOOD ESTIMATION;

SURFACE ANALYSIS;

EID: 84875830932     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.87.032716     Document Type: Article

References (25)

1. S. S. Plotkin and J. N. Onuchic, Q. Rev. Biophys. 35, 111 (2002).
2. J. N. Onuchic and P. G. Wolynes, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2004.01.009 14, 70 (2004).
3. P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science SCIEAS 0036-8075 10.1126/science.7886447 267, 1619 (1995).
4. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, Annu. Rev. Biophys. 1936-122X 10.1146/annurev.biophys.37.092707.153558 37, 289 (2008).
5. J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco, and C. Bustamants, Science SCIEAS 0036-8075 10.1126/science.1058498 292, 733 (2001).
6. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(74)80109-0 28, 578 (1974).
7. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic Press, New York, 2003).
8. M. de Messieres, B. Brawn-Cinani, and A. La Porta, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2011.03.067 100, 2736 (2011).
9. H. A. Kramers, Physica PHYSAG 0031-8914 10.1016/S0031-8914(40)90098-2 7, 284 (1940).
10. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.63.1195 63, 1195 (1989).
11. S. Kumar, J. M. Rosenberg, D. Bouzide, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540130812 13, 1011 (1992).
12. E. M. Boczko and C. L. Brooks, Science SCIEAS 0036-8075 10.1126/science.7618103 269, 393 (1995).
13. N. A. Denesyuk and J. D. Weeks, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.102.108101 102, 108101 (2009).
14. R. Zhu and G. Hummer, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.21989 33, 453 (2011).
15. J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theor. Comput. 1549-9618 10.1021/ct0502864 3, 26 (2007).
16. J. Marko and E. Siggia, Macromolecules MAMOBX 0024-9297 10.1021/ma00130a008 28, 8759 (1995).
17. L. Green, C.-H. Kim, C. Bustamante, and I. Tinoco Jr., J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2007.05.058 375, 511 (2008).
18. Z. Yu, J. D. Schonhort, S. Dhakal, R. Bajracharya, R. Hegde, S. Basu, and H. Mao, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja806782s 131, 1876 (2009).
19. M. de Messieres, J.-C. Chang, B. Brawn-Cinani, and A. La Porta, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.109.058101 109, 058101 (2012).
20. C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 2690 78, 2690 (1997).
21. G. E. Crooks, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.61.2361 61, 2361 (2000).
22. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.071034098 98, 3658 (2001).
23. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.1015661107 107, 21441 (2010).
24. E. Evans, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.30.1.105 30, 105 (2001).
25. O. K. Dudko, G. Hummer, and A. Szabo, Proc. Nat. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0806085105 105, 15755 (2008).